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From 2013.igem.org

Contents 1 Week 1: May 28 - May 31 2 Week 2: June 3 - June 7 3 Week 3: June 10 - June 14 4 Week 4: June 17 - June 21

Week 1: May 28 - May 31

• Tuesday, 5/28: Today began with the Summer Science Research Orientation, and afterwards I attended the HCI Lab Summer Orientation where everyone was given a brief overview of Human Computer Interaction, as well as the design process that we’ll be following. Then, after a group lunch, we dived straight into the research. I was paired up with Heather, and our project is dubbed the “art project,” tailored towards non-scientists. Here, our goal is to communicate core concepts of synthetic biology, as well as showing off the excitement, risk, and promise of cutting-edge technology.

• Wednesday, 5/29: Our research continued as we spent the bulk of the morning and afternoon reading about the various synthetic projects that are out there. Heather and I went through many different websites and articles, building up a reservoir of files as we familiarized ourselves with these projects and tried to draw inspiration. Later in the afternoon, we switched over to the more technical side of our project. Since we are trying to incorporate sifteo cubes into our project, we spent the bulk of the afternoon and evening playing with the code in the example files that came with the installation, and trying to make sense of the code.

• Thursday, 5/30: Today the Wellesley HCI lab headed into Boston for our first experience with wet lab training. At MIT, we met Prof. Natalie Kuldall who walked us through the BioBuilder workshop. There, we received an introduction to synthetic biology and the most fundamental concepts such as standardization, abstraction, and synthesis. It was exhilarating, and definitely a mind-opener to everything that this field has to offer. Before, we had only the readings to provide us background, but the workshop definitely made the topics a lot more clearer.
• Later, we were also given the opportunity to actually enter the wet lab environment. Hands-on learning is the best sort of learning, so it was great being in a lab to actually conduct some critical experiments. My partner was Heather, and we gave them our best shot! And while we may not have been the best synthetic biologists, we did make several key observations.

• First, especially for nonscientists, it’s important to communicate the lab instructions clearly. Often, we found the directions confusing and had to constantly ask for clarification. Part of it was because we simply didn’t understand the terminology or conventions. At one instance, Natalie mentioned herself that she should have included instructions saying “mix the resulting solution.” As scientists, she told us that they always just automatically mix solutions so that repeating them in a lab instruction is repetitive as it’s an assumed action. But as nonscientists, it’s a connection that we would not have made.
• In addition, while we were able to conduct the experiments simply by following directions, it was difficult at times for us to actually gauge what it was that we were doing. If there could be some sort of explanation perhaps at the side that you could read to see how all the pieces fit together, I think that would be greatly beneficial. This would be a great application of the “drawer” idea on a surface; when confused, you could click on a symbol or something and have an explanation pop up that then minimizes so that you can continue your experiment after you’re done reading.
• All in all, it was an eye-opening experience. We concluded the day with a summary and reflection of what we had learned, and since the project Heather and I are working on is concerned with making synthetic biology accessible to nonscientists, we have a lot of new information to work with and incorporate into our thinking!

• Friday, 5/31: After our wet lab experience at MIT yesterday, today was spent back at the HCI lab where we continued our research for our projects. In the morning, Heather and I continued our work with the sifteo cubes and started altering the code as well, seeing if we could rewrite parts of the code to get it to do what we wanted. In the afternoon, we shifted gears once again and started brainstorming actual ideas that we could implement for our project. We came up with three: extending synflo, replicating the glowing tree experiment, and creating a game.

Week 2: June 3 - June 7

• Monday, 6/3: Today the HCI lab met with the BU igem team! In the morning we were given a more detailed overview of synthetic biology that went beyond the core big ideas of standardization, abstraction, and synthesis. Then, after a group lunch, we completed the Eugene Tutorial, where Eugene is a new language readable by both machines and humans meant to speed up and innovate the design of novel biological devices. To me, it was incredibly exhilarating to see how similar it was to the Java programming language. After the tutorial, I worked with Diana and Pooja to write a program that would return the result dictated in an image that was sent to us. It was great practice and afterwards I felt like I had a very solid foundation in this language.

• Tuesday, 6/4: Another day was spent with the BU igem team as we each went over the projects that we were working on. In the morning, BU presented their projects, and after lunch the Wellesley team did their presentations. More time was then spent learning Eugene as we tried to modify and add rules to improve the program we had worked on yesterday. Then, we went on a tour of the BU team’s wet lab, and concluded the day with some bonding over bowling at Jillian’s!

• Wednesday, 6/5: Today was spent back at the HCI lab. Heather and I continued our research in the morning, seeing if we could draw up even more ideas that we could add to our current three. Then, in the afternoon, we started fleshing out some sketches in an attempt to solidify some of those ideas. We ran into some trouble here and there, but I made sure to take down lots of notes, which we will definitely discuss during our stand-up meeting tomorrow.

• Thursday, 6/6: Heather and I met up with Orit to discuss our progress thus far with the “art project.” After explaining our three main ideas, Orit suggested that we also focus on concepts, and not just content. In other words, the ideas that we want to communicate, such as modularity, abstraction, protocol, safety issues, even the fact that things can go wrong! We got a lot of feedback on extending Synflo, such as looking into a device that can create scents (for the banana lab!), and got great new groundwork done as well on replicating the glowing trees experiment (creating a projection, something that will be very aesthetically pleasing). For now, we have a lot of new ideas to work with, and will be following those through!

• Friday, 6/7: Today, Heather and I continued our discussion of possible ideas to implement. Only today, we focused more on sketches and drawing out our ideas onto paper. We made good progress, and it was really great that Casey was there to mentor us as well. We added another possible idea to our arsenal – a time capsule like program where people can code a message in bacteria! And with Casey’s help, we also got a new perspective on the game design we are thinking about implementing (a tribute to Conway’s game of life). In addition, we also drew out a really great sketch of how we envision our glowing tree idea to look.

Week 3: June 10 - June 14

• Monday, 6/10: Today, Heather and I met up with Orit and discussed all the ideas we had generated over the past several work days. During that time, we focused a lot on width and coming up with as many possible ideas as we could. Then, after our talk with Orit, she mentioned that we had a very good arsenal, and that it was time to pick three and start focusing on depth rather than width. Heather and I chose to explore the glowing tree idea, the time capsule idea, and the game idea.

• Tuesday, 6/11: Heather and I started working on depth yesterday afternoon after our meeting with Orit, and continued doing so this morning. Then, later in the day, we had another check-in with our advisor. For the glowing tree idea and the time capsule idea, we looked more into the actual lab procedures and for the game idea, we started thinking about various different options of implementation that would still render the game collaborative and dynamic. We presented our thoughts to Orit, and she suggested that start storyboarding and thinking more about interfaces now that our ideas were solid.

• Wednesday, 6/12: After spending yesterday afternoon storyboarding our three main ideas, we met up with Orit yet again to show her our work. We knew that our lab procedure for the glowing tree idea was way too long, and Orit agreed; she suggested that we go through the lab procedure once more and to this time, capture the big ideas. Thus, we started a new storyboard for that experiment. We also redrew the storyboard for the time capsule idea, adding more details we had skipped over in our initial draft. Lastly, we unfortunately ran out of time to discuss our game idea (which was a slight bummer since we were a little stuck on it), but we will definitely talk more about it during our meeting with Orit tomorrow.

• Thursday, 6/13: This morning Heather and I finalized our first draft storyboards and set about printing out all the inspiration and initial research materials we had gathered online. Then, in the afternoon, we started working on our final draft storyboards for tomorrow’s presentation and brainstorming session with BU. Once we had finished, we headed upstairs to room 211 to pin up all of our papers in preparation for tomorrow.

• Friday, 6/14: Today we had a very fruitful brainstorming session with the BU igem team. It was exhausting work, but we were very productive and got tons of great feedback from all of the people who came. In the morning, the people from BU were split into three groups, and circled around the room to hear each Wellesley project group present their projects. After a lunch break, we then reconvened and discussed the suggestions people had made in the morning so that more brainstorming could be done as an entire group. For our project, personally, Heather and I received great feedback on both the glowing plant and the time capsule ideas. One such example was including a guest book after the experiments to log down how people feel about these new, innovative ideas. All in all, it was a fantastically productive day, and we are eagerly looking forward to next week and the next stage of implementation.

Week 4: June 17 - June 21

• Monday, 6/17: After the big presentation to BU last Friday, Heather and I met up today ready to dive into the next stage of the design process. In the morning, we refreshed ourselves with everything that was said on Friday including suggestions, advice, and general comments. Afterwards, we met with Orit, who told us that today was a day of decisions. We were stuck between the glowing tree experiment and the time capsule idea, but in the end, we felt more excited about the latter and thus our project was chosen! The rest of the day was spent with power storyboarding – really mapping out the exact process, environment, and layout of how we envisioned our project unfolding. However, towards the end of the day, we were reminded that regionals were taking place in Canada! – there wasn’t really any way we could bring all the surfaces we had planned on using all the way to Toronto. Thus, we had to reconsider our plan to adapt to this problem of portability, which is what we spent the rest of the evening considering.

• Tuesday, 6/18: Because of the portability issue, Heather and I were forced to reevaluate how we envisioned our project, and thus wanted to meet with Orit to discuss this new facet. In the end, however, we were told that this was our decision, and that Orit would be fine with either or. After some further clarification with Consuelo and some advice from Diana, Heather and I decided to go with one core layout, but three different behaviors depending on which method people choose to interact with (ie: web application with simple mouse interaction; surface with touch sensors; projection from web application – mainly for the demo). After coming to a decision, it was time to move onto the implementation. Heather started working on mockups, and I started researching the twitter API.

• Wednesday, 6/19: